Industry critics have long feared Atlantic salmon raised in open-net cages in the ocean can pass on diseases to wild salmon and as a result, jeopardize those wild stocks.
But an outbreak of infectious haematopoietic necrosis, known as IHN, on an Atlantic salmon farm off Vancouver Island's west coast in May appears to have been caused by passing wild stocks, a reversal of the traditional arguments against the industry.
Instead of harming wild stocks, the May outbreak actually led to the quarantine of Mainstream Canada's Dixon Bay farm, north of Tofino, the cull of more than 560,000 young Atlantic salmon, and fears of a larger outbreak industry-wide.
The all-clear bell was rung by the BC Salmon Farmers Association on Friday, when it announced that independent tests for the virus on all active Atlantic salmon farms in the province have now come back negative.
But farms will continue to watch and test their fish, the association announced.
"Any infectious agent has the potential to cross from fish to fish, and some of those fish might be outside the pen and some of those fish might be inside the pen," said Gary Marty, a veterinarian and fish pathologist for B.C.'s Ministry of Agriculture.
"We have to assess each infectious agent individually."
Native to Pacific waters, IHN can cause death in young finfish raised in freshwater hatcheries, juveniles recently introduced to sea water and older finfish raised in sea water, states the Canadian Food Inspection Agency on its website.
About 20 species found in the natural environment, including pink, chum, coho, sockeye and Atlantic salmon, as well as Pacific herring, are susceptible to infection, as well, the agency adds.
But Marty said while Pacific salmon have developed a natural resistance to the virus, which means they can be infected but not show any signs of infection or even die, Atlantic salmon have not.
"It basically kills the blood forming cells in the fish, and that includes white blood cells so the fish cannot fight disease, and red blood cells which carry oxygen," said Marty. "Both things essentially shut down. The fish dies."
Vaccines for IHN are available, but Mainstream Canada did not vaccinate fish at the company's Dixon Bay farm, said Marty.
Fears about IHN and its impact on the industry emerged for the first time in nearly a decade when Mainstream Canada reported May 15 that third-party tests results had detected it at a farm, later identified as Dixon Bay.
The food inspection agency quarantined the site, and the company announced plans to cull its salmon, which were then transported to a composting facility in Port Alberni, B.C.
Two other B.C. farms were also quarantined briefly, but those quarantines were lifted after followup testing failed to detect the virus.
In the midst of the scare, the industry announced heightened bio-security procedures to prevent the spread of the virus from farm to farm.
While the cost of the outbreak and scare to Mainstream remains unknown, it won't be minuscule,
Laurie Jensen, a Mainstream spokeswoman, said previously that in addition to the cull, the company had to absorb the costs of cleaning the site and replacing equipment like nets that couldn't be disinfected.
Larry Hammell, a professor of aquatic epidemiology at the University of Prince Edward Island, said he's predicting more outbreaks because the virus cycles every seven to 10 years.
"Once you get it in this one exposure, it probably means that there's wild populations out there that have a slightly higher infection prevalence this coming season," he said.
The origins of the virus remain uncertain, said Sonja Saksida, executive director and researcher at the Centre for Aquatic Health Sciences, in Campbell River, B.C..
Based on studies of its genotype, though, she suspects it came from sockeye salmon migrating from Washington state.
"The more likely source is some population of out-migrating sockeye salmon smolts because, I mean, this is, you know, we generally call it sockeye disease," said Saksida, who studied the last outbreak of IHN between 2001 and 2003.
"It's a very common pathogen affecting sockeye salmon."
She said the virus can spread through feces and mucus, and then it becomes a problem for other Atlantic salmon farms, much like the 2009 outbreak of avian influenza in B.C.'s Fraser Valley poultry industry.
Thousands of birds were destroyed because of that outbreak.
In contrast, the last outbreak of IHN led to the destruction of about 19 million Atlantic salmon, said Saksida.
With one outbreak under control, Saksida suggests now may be the time to do a broader examination of what viruses are in the marine environment.
She said some studies are taking place by federal fisheries officials in the Strait of Georgia and the Discovery Islands, but they need to be expanded.
"Obviously water transmission of pathogens can be a problem," she said. "So if you do have a problem you want to know how something's going to move in the water.
"But you also need to know what's out there. So I think doing some kind of wild fish surveillance and trying to figure out what they have, when they have it, if they have it is really important."